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PRJNA195909:zebrafish embryo and larva development
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Results for rfx3_rfx2+rfx4
Z-value: 3.72
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Transcription factors associated with rfx3_rfx2+rfx4
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
| ENSDARG00000014550 | regulatory factor X, 3 (influences HLA class II expression) | |
| ENSDARG00000013575 | regulatory factor X, 2 (influences HLA class II expression) | |
| ENSDARG00000026395 | regulatory factor X, 4 | |
| ENSDARG00000116861 | regulatory factor X, 4 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| rfx4 | dr11_v1_chr18_-_15373620_15373620 | 0.95 | 6.8e-05 | Click! |
| rfx3 | dr11_v1_chr10_-_625441_625441 | -0.91 | 5.4e-04 | Click! |
| rfx2 | dr11_v1_chr8_-_20118549_20118549 | -0.87 | 2.6e-03 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr2_+_68789 Show fit | 22.05 |
ENSDART00000058569
|
claudin 1 |
|
| chr9_-_712308 Show fit | 9.66 |
ENSDART00000144625
|
NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3 |
|
| chr24_-_205275 Show fit | 7.87 |
ENSDART00000108762
|
VOPP1, WBP1/VOPP1 family member |
|
| chr8_+_21195420 Show fit | 7.40 |
ENSDART00000100234
ENSDART00000091307 |
collagen, type II, alpha 1a |
|
| chr23_+_35708730 Show fit | 5.64 |
ENSDART00000009277
|
tubulin, alpha 1a |
|
| chr6_+_612330 Show fit | 5.45 |
ENSDART00000166872
ENSDART00000191758 |
kynureninase |
|
| chr16_-_45069882 Show fit | 5.38 |
ENSDART00000058384
|
glyceraldehyde-3-phosphate dehydrogenase, spermatogenic |
|
| chr21_+_26697536 Show fit | 5.32 |
ENSDART00000004109
|
guanine nucleotide binding protein (G protein), gamma 3 |
|
| chr5_-_71705191 Show fit | 4.67 |
ENSDART00000187767
|
adenylate kinase 1 |
|
| chr6_-_8736766 Show fit | 4.63 |
ENSDART00000143956
|
caveolae associated protein 2b |
Network of associatons between targets according to the STRING database.
First level regulatory network of rfx3_rfx2+rfx4
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.4 | 19.3 | GO:0070830 | apical junction assembly(GO:0043297) bicellular tight junction assembly(GO:0070830) |
| 0.5 | 11.1 | GO:0032981 | NADH dehydrogenase complex assembly(GO:0010257) mitochondrial respiratory chain complex I assembly(GO:0032981) mitochondrial respiratory chain complex I biogenesis(GO:0097031) |
| 0.1 | 8.7 | GO:0006165 | nucleoside diphosphate phosphorylation(GO:0006165) |
| 0.9 | 8.5 | GO:0021631 | optic nerve morphogenesis(GO:0021631) |
| 0.2 | 8.0 | GO:0030199 | collagen fibril organization(GO:0030199) |
| 0.0 | 7.6 | GO:0046777 | protein autophosphorylation(GO:0046777) |
| 1.8 | 5.3 | GO:0097053 | L-kynurenine metabolic process(GO:0097052) L-kynurenine catabolic process(GO:0097053) |
| 0.1 | 5.3 | GO:0003341 | cilium movement(GO:0003341) |
| 0.9 | 4.7 | GO:0060296 | regulation of cilium movement involved in cell motility(GO:0060295) regulation of cilium beat frequency involved in ciliary motility(GO:0060296) regulation of cilium-dependent cell motility(GO:1902019) |
| 0.7 | 4.7 | GO:0009180 | ADP biosynthetic process(GO:0006172) purine nucleoside diphosphate biosynthetic process(GO:0009136) purine ribonucleoside diphosphate biosynthetic process(GO:0009180) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 18.2 | GO:0005923 | bicellular tight junction(GO:0005923) occluding junction(GO:0070160) |
| 0.0 | 13.4 | GO:0005615 | extracellular space(GO:0005615) |
| 0.3 | 11.5 | GO:0045271 | mitochondrial respiratory chain complex I(GO:0005747) NADH dehydrogenase complex(GO:0030964) respiratory chain complex I(GO:0045271) |
| 0.0 | 9.5 | GO:0030659 | cytoplasmic vesicle membrane(GO:0030659) |
| 0.1 | 8.5 | GO:0005581 | collagen trimer(GO:0005581) |
| 0.0 | 6.7 | GO:0005874 | microtubule(GO:0005874) |
| 0.3 | 5.3 | GO:0031680 | G-protein beta/gamma-subunit complex(GO:0031680) |
| 0.0 | 3.9 | GO:0005814 | centriole(GO:0005814) |
| 0.3 | 3.8 | GO:1990246 | uniplex complex(GO:1990246) |
| 0.1 | 3.8 | GO:0022627 | cytosolic small ribosomal subunit(GO:0022627) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 26.6 | GO:0005198 | structural molecule activity(GO:0005198) |
| 0.0 | 13.5 | GO:0005509 | calcium ion binding(GO:0005509) |
| 0.1 | 8.8 | GO:0005201 | extracellular matrix structural constituent(GO:0005201) |
| 0.1 | 8.4 | GO:0005212 | structural constituent of eye lens(GO:0005212) |
| 0.0 | 6.5 | GO:0003924 | GTPase activity(GO:0003924) |
| 0.2 | 6.3 | GO:0017075 | syntaxin-1 binding(GO:0017075) |
| 0.4 | 5.8 | GO:0004017 | adenylate kinase activity(GO:0004017) |
| 0.1 | 5.8 | GO:0005200 | structural constituent of cytoskeleton(GO:0005200) |
| 1.3 | 5.4 | GO:0004365 | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity(GO:0004365) glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity(GO:0043891) |
| 1.1 | 5.3 | GO:0016823 | hydrolase activity, acting on acid carbon-carbon bonds(GO:0016822) hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances(GO:0016823) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.8 | 22.1 | PID NECTIN PATHWAY | Nectin adhesion pathway |
| 0.2 | 6.5 | ST DIFFERENTIATION PATHWAY IN PC12 CELLS | Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. |
| 0.1 | 4.1 | PID NOTCH PATHWAY | Notch signaling pathway |
| 0.0 | 3.5 | NABA SECRETED FACTORS | Genes encoding secreted soluble factors |
| 0.0 | 2.3 | NABA ECM REGULATORS | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix |
| 0.1 | 1.9 | PID LIS1 PATHWAY | Lissencephaly gene (LIS1) in neuronal migration and development |
| 0.1 | 1.7 | PID ILK PATHWAY | Integrin-linked kinase signaling |
| 0.1 | 1.2 | ST PHOSPHOINOSITIDE 3 KINASE PATHWAY | PI3K Pathway |
| 0.0 | 0.9 | ST INTEGRIN SIGNALING PATHWAY | Integrin Signaling Pathway |
| 0.0 | 0.8 | PID ARF6 PATHWAY | Arf6 signaling events |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 2.5 | 22.1 | REACTOME TIGHT JUNCTION INTERACTIONS | Genes involved in Tight junction interactions |
| 0.2 | 11.0 | REACTOME RESPIRATORY ELECTRON TRANSPORT | Genes involved in Respiratory electron transport |
| 0.4 | 5.6 | REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY | Genes involved in Post-chaperonin tubulin folding pathway |
| 0.3 | 5.4 | REACTOME GLYCOLYSIS | Genes involved in Glycolysis |
| 0.4 | 5.3 | REACTOME TRYPTOPHAN CATABOLISM | Genes involved in Tryptophan catabolism |
| 0.3 | 5.3 | REACTOME THROMBOXANE SIGNALLING THROUGH TP RECEPTOR | Genes involved in Thromboxane signalling through TP receptor |
| 0.2 | 4.7 | REACTOME SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES | Genes involved in Synthesis and interconversion of nucleotide di- and triphosphates |
| 0.0 | 4.3 | REACTOME PEPTIDE CHAIN ELONGATION | Genes involved in Peptide chain elongation |
| 0.4 | 2.3 | REACTOME SIGNALING BY FGFR3 MUTANTS | Genes involved in Signaling by FGFR3 mutants |
| 0.2 | 2.2 | REACTOME ACTIVATION OF BH3 ONLY PROTEINS | Genes involved in Activation of BH3-only proteins |